New Beginnings
by Kayleen143
Summary: John never talked about his past. No one knows about his family or old friends. So what happens when someone from his past shows up on Atlantis?
1. Chapter 1

**A/N: Hey guys welcome to my story. I hope that you enjoy it! *Revised Chapter**

Chapter One

"Offworld activation" Chuck's voice rang out through the gate room.

"So whose this new scientist?" John asked Rodney as they walked down the steps to the gate.

"She's an amazing person as well as being a great scientist. Seriously you should read some of her work. It's amazing!"

"You sound like you're in love Rodney."

"I'm telling you , she's my kinda girl so stay away Sheppard."

"What? You know I don't really go for girls who I can't understand what they're saying half the time."

"Oh but I think you might be tempted with this one. She is really hot, I mean smoking."

"Thank you for that assessment, Dr. McKay is it?"

Both John and Rodney turned to see a beautiful woman standing there.

"Uh, oh, I mean no problem." Rodney stammered.

The woman turned to John, "Hello John, long time no see."

"Uh do I know you? Cause I'm pretty sure I would remember if I did."

"Yes of course you've met me before...John its me, Rachael."

"Rachael?!"

"Whoa whoa wait. You two have met before?"

"Yes we have. I grew up with her." John said shocked.

"Oh, there goes my luck out the window! How come you always are friends with the hot girls?"

"We're not friends, Dr. McKay." Rachael said, "In fact you could say-"

"We're friends" John interjected. "Uh Rae? Can I talk to you for a minute?"

"You're talking to me now."

"I mean in private."

"Sure you could escort me to my quarters."

"Sure! Uh Rodney-"

"She's on the same level as you. Its the only empty room on your level."

"Uh thanks. This way Rae." John walked away with Rachael close behind him.

"Yep no problem." Rodney sighed as they walked away. "This is so not fair."

"So what did you want to talk to me about?" Rachael asked as soon as they were out of hearing range.

"Uh just ya know, two old friends catching up and that kinda stuff."

"If I remember correctly, last time I saw you, you said you wanted to never see me again. Why the sudden change of heart?"

"Well my friends here don't really know anything about my past."

"Well you were always kind of private."

"And uh, we didn't exactly end on the best of terms."

"No kidding."

John sighed, "I'm commanding military officer of this base and I need to at least be on speaking terms with everybody. So...let bygones be bygones?"

"Is this an apology John?"

"NO! I have no need to apologize!"

"Yes you do! Do you have any idea of what you did to me?!"

"You overreacted! You know, I am allowed to have friends besides you!"

"I didn't have a problem with you having other friends! I really didn't! I had other friends beside you too! I just had a problem with you ditching me just because your girlfriend didn't like me!"

"She had a darn good reason not to like you! All those things you said to her! You were a jerk to her Rae!"

"She was lying! I never said any of those things! And it just kills me that you believed her and not me! We've know each other our whole lives John!"

"You were just jealous!"

"Yes I was jealous! I didn't like her taking up so much of your time that you didn't have any for me. But I wouldn't say any of those things to her. I thought you knew me better than that!" Rachael's voice began cracking and tears threatened to spill. "You were my best friend and I didn't want to lose you."

"Rae I don't want-"

"Save it John. You didn't care then and you apparently don't care now. Just show me where my quarters are."

They walked in silence for a while until John stopped in front of a door.

"Here's your quarters." John said.

"Thanks."

"Need any help?"

"Nah I got it."

"Okay." John turned to walk away,

"Jo-uh Col. Sheppard"

He turned around. "What?"

Rachael's eyes were red from crying. "What time do I report for duty tomorrow?"

"You're coming with my team for a mission, briefing is at 0800."

"Okay"

***The next day***

"Dr. Rachael Blake, I have read through your file and am pleased that you asked to be transferred here." Mr. Woolsey said, "You seem to be a very bright women. Welcome aboard doctor."

"Thank you Mr. Woolsey, and please, just call me Rachael."

"Well, Rachael, are you ready for your first briefing on Atlantis?"

"That I am sir." Rachael gave him a bright smile and settled into her chair as he began to talk.

Rachael looked around at the people around the table. There was Dr. Rodney McKay, the head scientist and from what she'd been told, a bit on the arrogant side. Then there was Teyla, the beautiful Athosian women who had asked her to lunch someday, Ronon, the strong, silent member of the team who seemed to take everything in with a warrior's mindset. And finally there was John, the leader of the team and, in her mind, still one of her best friends. She had to admit that whoever made the decision to make him CMO, had chosen wisely. John was fiercely loyal and made sure they never left a man behind. He had been like that his whole life. Rae gave a small smile at the memories she had of growing up. She remembered swimming in the small lake behind their houses, running races, playing hide and seek in the woods. She remembered just opening her arms and letting him fall into them at his mom's funeral. She remembered his girlfriend's smug smile as John confronted her about what she had supposedly said. She remembered yelling and crying at John as they fought, both of them saying mean things. John had yelled at her to

"Get out of my life!" and

"Stop trying to keep me for yourself!"

So she had left, she graduated early and went to an out of state college, never looking back...until now.


	2. Chapter 2

**A/N: Revised chapter**

Chapter Two

John looked across the table and saw Rae staring at him. Their eyes met briefly before hers flicked away. He watched as her cheeks turned pink. He smiled as he thought of the last time he had saw her get embarrassed. They had been eating lunch together when Steven Jacobs had come over to their table. Stuttering, he said hi to Rae, then asked if she wanted to go to the Spring Fling Dance with him. She had blushed beet red, then said yes. When Steven had walked away with a big smile on his face, Rae had turned to John, face still red. "Shut up." She had said to the knowing grin on his face.

John still grinned at the memory then shook his head. What was wrong with him? This was the girl who told his girlfriend that she was a slut and that she could go die in a hole. He had believed her. When he had confronted Rae, she had told him she hadn't said those things. He didn't know what to believe. On one hand he had his extremely hot girlfriend, whom he loved and on the other he had the girl he had known his whole life. When his girlfriend in tears had told him that if he didn't stop talking to Rae then she would break up with him, he had chosen to stay with her. Rae had, in tears, run away. He never saw her again...until now. What was she doing here? Woolsey said she asked to be transferred here. Did she find out he was here and came for him? No, no Rae had seemed like she never wanted to see him again either. She wouldn't purposely come here just to see him. So then why was she here?

Rae saw John smile then shake his head and glance at her, she quickly refocused her attention on Mr. Woolsey, who was saying something about an interference on the planet they were going to. What was John thinking?

"Dr. Blake?" Woolsey's voice pulled her back to reality,

"Yes Mr. Woolsey?"

"What do you think about this interference? Dr. McKay seems to think its a natural occurrence, do you concur?"

Rae looked at the data displayed on the screen. "Hmmm...it's seems to be, but wait! See that?!"

"What?!" McKay asked, moving up to stare at the screen.

"There!" Rae said, moving to point at the screen. "That inconsistency, it looks like an EMP but theres something different about it..."

"You're right, it almost like-"

"Oh no, you don't think?"

"We need-"

"-to check this out."

They both moved to leave the room when Woolsey cleared his throat. "Excuse me doctors, what is going on here?"

They both stopped short. "That inconsistency could be harmful radiation. We need to figure out if it is before we go."

"Alright then, go ahead."

Rae and McKay left the room, mumbling to each other, hands animated.

"Hey geeks what's up?" John asked as he walked into McKay's lab. Rae and McKay glared at him, "Hey I was just asking a question." John said defensively.

"Nothing's up that's what." Rae said. "I've never seen this kind of radiation before. I don't know if it's harmful or not."

"Well how long is it going to take to figure out? Woolsey is getting impatient."

Rae sighed. "He's going to have to wait, unless he's willing to send us to a planet with potentially harmful radiation."

John shook his head. "Rodney what do you think?"

Rodney pushed himself away from the table, "She's right, this radiation is similar to gamma-"

"-but it's not quite-"

"-the same. The only way-"

"-to know for sure would-"

"-would be to go there." Rodney and Rae looked at John after they finished

. "Did you guys just finish each other's sentences?"

"Yes." They said simultaneously.

"Okay, just a little weird, so I should tell Woolsey that we should go to this planet?"

"In hazmat suits." Rae answered.

"Okay, start getting your crap together."

"It isn't crap." Both Rodney and Rae muttered under their breath. John smirked as he walked out.


	3. Chapter 3

**A/N: Revised chapter**

Chapter Three

"Good luck." Woolsey's voice came over the radio. "And come back if anything is out of the ordinary."

"Sir, we're on an alien planet, things aren't going to be normal." John answered.

"You know what I mean Colonel."

"Yes sir." The Stargate closed. "Alright let's move out." John took point and lead the way forward.

The world they were on was strange. The whole area was covered in strange colored tall grass, well over Ronon's head. Both Rodney and Rae were reading their instruments, muttering under their breaths as they did.

"You got anything?" John asked the two scientists who were huddled over a tablet.

Rae looked up, "We can now say that the radiation isn't harmful if we don't stay too long."

"Are you sure? You were saying it was gamma radiation early."

"It's very similar, almost exactly alike, but nowhere near as harmful."

"Do we still need these things?" Ronon asked, lifting his arms to show the hazmat suit.

"No they aren't necessary." Rodney replied.

"Great." Ronon took off his suit and the others followed.

"The air smells...sweet." Teyla commented.

"Yeah it does." John agreed, "Is that going to be a problem?"

"Nope." Rae said.

"Alright stay alert." John moved forward.

After walking for a while Teyla said, "Colonel, would it not be more effective if we went in different directions?"

John stopped and wiped his forehead. "Yes I think so, especially if we don't want to stay that long." He looked to Rae for confirmation.

"Right, we should only stay a few more hours."

"Alright you heard her, we will be leaving in two hours, stay in radio contact and meet back here when it's time to go." John ordered as they started to move out.

He watched as Rae readjusted the straps on her backpack and made sure her gun was loaded. He made eye contact as she looked up. She gave him a glare then turned on her heel into the woods.

Rae drew in a deep breath as she walked away from John, that was the second time today she had caught him staring at her. What was going on? She hadn't felt like this since high school...

**Flashback:**

_John and Rae were laying out on a deck in the middle of a lake. They were both laughing as John was trying to push Rae in. When he finally succeeded, he did a little victory dance. Then he noticed Rae hadn't come back up yet. He started calling her name, bending over the edge of the dock. Suddenly, Rae's hand shot out of the water and pulled him in. They both came up laughing,_

_"Don't ever do that again!" John said to her, "I thought you were hurt or something."_

_"Sorry." She grinned, mischief dancing in her eyes._

_"What?" John asked._

_"Nothing!" She answered in a singsong voice as she grabbed a pair of googles then dived under._

_He shook his head, grabbed another pair, then followed her. The lake was clear and he could see her swimming up ahead. She turned around and beckon him closer. As he swam towards her, he noticed how beautiful she looked, her hair spread out around her. He reached her and did something he had never done before, he reached out and pulled her close. He saw the look of confusion in her eyes and before he could think twice, he bent forward and kissed her. She didn't know what to do but then instincts took over. She deepened the kiss and wrapped her arms around him. They stayed like this, suspended in water, until they had to come up for air. When they resurfaced, they stared at each other until Rae broke the silence._

_"Well," she said, "that was nice."_

_Then she swam away and went home. The next day they acted like nothing happened. But in Rae's heart, something big had happened. She realized she had fallen in love with her best friend._

***End Flashback***

Rae stopped to take some samples of a plant when she heard a scream. Her supplies fell to the ground as she ran towards the scream. She ran through the forest until she burst out of the thickness, and out over the edge of a cliff.

John reached down and grasped Teyla's wrist and pulled her up.

"Are you okay?" John asked her.

"I believe so." Teyla said, slightly out of breath.

Suddenly they heard a scream. They looked at each other,

"That sounded like Rachael." Teyla said,

"John wait!" She yelled after him as he bolted off, calling Rae's name.

He ran and ran, nothing could stop him from getting to her. "Rae! Rae!" He screamed, stopping in the middle of a clearing. "Rae!"

"Shepard!" he heard Ronon yell. "Over here!"

He ran towards Ronon's voice, "Whoa! Stop Shepard!" Ronon's arm came out of nowhere and stopped John from falling off the cliff.

"Where is she?" John asked, breathing heavily.

"She's down there." Ronon said, pointing over the edge.

John started to move towards the edge but Ronon stopped him. "You might not want to look, it's not pretty."

John glared at Ronon until he let him go. He looked over the edge and saw Rae lying on a ledge about thirty feet down, her body bent awkwardly.

"Rae!" he called down to her. She stirred slightly, "She's still alive!" He began to look for a way down, "How are we going to get to her?" he asked Ronon, who was looking over the edge.

"Can't," he said, "we have to go back to the Stargate to get help."

"We just can't leave her down there all alone!"

"We don't have to, you stay here and I'll go get help."

"Okay." John said, his breath coming in short bursts, "Okay" he said again, calming himself down. "Go get help, and hurry!" he called after Ronon's retreating back. "Rae, help is coming, help is coming." he called down to her still form.

Pain, that's all she could feel. Pain making her body throb. She could hear a voice, calling her name. She forced her body to move, crying in pain as she did so.

"Rae," the faint voice called, "help is coming, help is coming."

"Good." she thought, "I don't know how much more pain I can take."

The voice called down to he again, telling to try not to move and that they would have her out of here in no time. She tried to place the voice in her mind, it sounded very familiar and she felt comforted by it. She could hear the pain in it, the worry, even though she could hear him trying to be strong. Him...she decided it was a man talking to her, saying comforting words, it helped take her mind off the pain. What was he saying now? It seemed like he was telling a story, one that included both of them it seems. A story about what happened when they were young. He kept talking and laughing, his voice choking up sometimes. Then she recognized the voice,

"John..." she whispered, then her world went black.


	4. Chapter 4

**A/N: Revised chapter**

Chapter Four

John paced impatiently around the infirmary, waiting for news on Rae. They had been back for hours, Rae had been rushed straight to the infirmary and hadn't come out yet. Dr. Jennifer Keller came out of surgery and was immediately surrounded by the team.

"What's wrong?"

"Is she okay?"

Questions filled the air as the team drilled the doctor for information.

Keller held up her hands, "Look, I know you are all worried about her. I will answer your questions, but first give some room, please!"

The team back away when she yelled the last word. "I just came out of a very difficult surgery, but.." she paused, "I think she will be alright. She's not out of the woods yet, but I'm confident she'll live."

The team breathed a sigh in relief.

"She's going to be okay?" John asked,

"Yes John, she'll be okay."

"Good." he said, "Let me know when she wakes up."

He turned on his heel and walked out of the room. Ronon moved to follow him,

"No," Teyla stopped him, "let him have some time alone."

Ronon looked at John's retreating back, "Fine." he said.

John couldn't get out of the room fast enough. His team had seen him fall apart and he didn't know how to deal with it. He found himself walking to his room, he opened the door and just stood there. Then he fell against the wall and sank to the floor. His eyes closed and he whispered a "Thank you." Rae was going to be okay. She was going to be okay. Could he still care for her after all these years? After all she'd done? Or what she supposedly had done, he didn't know what to believe. He had ended up breaking up with his girlfriend after he had found out she was cheating on him. Maybe she had lied about what Rae said. Now that he thought about it, she probably had. She probably had been jealous of his relationship with Rae and decided to do something about it.

"You are such an idiot John!" he yelled at himself. "Don't believe the girl you've know all your life! Ahhhhhhhh!"

He rammed his fists against the wall then he got up and tore his room apart. After he finished, he looked around with a look of satisfaction, then fell to the floor, passed out. A sweet smell flowed through the room.

"Dr. Blake? Dr. Blake?" A woman's voice floated into her conciseness, pulling her up out of the hazy dreamworld she had been in. She opened her eyes and saw a blonde-haired woman standing next to her.

"Hello," she said, "My name is Jennifer Keller, I'm the head medical doctor here, we haven't had a chance to meet yet."

"I've heard about you." Rae said, looking around the room to see if she recognized anybody, "Rodney told me about you."

"He did?" Keller laughed, "Why would he do that?"

"I think he likes you." Rae said, finally seeing someone she recognized, "And speaking of Rodney..."

Keller turned around, her face red. "Ah Rodney, you're here. Why don't you keep her company while I go let Col. Shepard know she's awake." Keller said, brushing past him.

"Did I do something?" Rodney asked Rae, looking flustered.

Rae laughed, "Oh Rodney, you are so clueless."

Rodney looked indigent, but softened when he saw Rae wince in pain. "Are you alright? Do I need to go get Keller?" he asked her, starting to walk away.

"No! I'm fine! Please, stay." she said, taking small breaths as she did so.

"Are you sure?" he asked, looking at her worryingly,

"I'm" *breath* "sure"

"I don't think you are. I'm going to get Keller." He walked off, calling Keller's name.

He found her still trying to reach John. "Hey Jennifer, I think something's wrong with Rachael, she's having trouble breathing."

"Oh no, I was afraid this was going to happen."

She ran into the room, where Rae was sucking in air but getting nothing. "Crap." Keller said under her breath.

"Marie! Prep her for surgery and bring in a breathing machine!" Marie ran off to do as she was told. Keller grabbed Rae's hand.

"You're going to be alright," she said soothingly. "you're going to be alright. Just keep trying to breathe."

"What's wrong?" Rodney asked, looking frantic.

"She has a blocked airway and maybe a collapsed lung." Keller answered, "Marie, where's that machine?!"

Marie hustled into the room, pushing the machine in front of her. Keller and her started hooking Rae up to it.

"This going to to help you breathe okay?" Keller explained.

Rae nodded and tried to stay conscious. Little black spots were appearing in her vision. Finally they got her hooked up and Keller turned it on. Rae took a big breath of air and starting gulping it up.

"Whoa, slow down. You need to take slow, deep breaths." Keller instructed. Rae obeyed.

"Oh man, oh man, oh man!" Rodney freaked out in the background.

"Rodney, why don't you go check on John? He wasn't answering his comm earlier." Keller told Rodney as she checked Rae's vitals.

"Good idea." Rodney rushed off to go find him.

"I think that freaked him out a little, don't you think?"

Rae tried to laugh but a gurgling sound came out instead.

"Hey no laughing allowed." Keller said sternly.

Rae gave her a sheepish look and shrugged.

"Hmmm, I'm going to put you under the scanner to see what's blocking your airway, okay?"

Rae nodded.

"Okay let's go."


	5. Chapter 5

**A/N: Revised chapter**

Chapter Five

"John? John?" Rodney called, tapping his comm as he did so. "John? John, please answer your radio."

When John didn't answer, Rodney sighed and decided to check John's quarters. As he walked to the nearest transporter, he bumped into Zelenka, literally.

"Watch where you're going Radek." Rodney snapped.

Radek looked like he was about to say something then decided against it. He muttered something in Czech under his breath and said, "What's wrong with him?"

Rodney stood outside of John's quarters, "John!" he yelled, swiping his hand in front of the door. "John!" he yelled again when John didn't answer.

He began banging on the door, yelling at John. He began to attack the door, screaming. Finally he exerted all of his energy and leaned against the door. He could smell something sweet just before he passed out and sank to the floor.

"Alright, the reason you had trouble breathing was because you had some fumes in your lungs." Keller explained to Rae, "I don't know what it is, I've never seen it before."

Rae looked up at her and shook her head, "I don't know," she said, "there wasn't anything wrong with the air...wait! The air smelled sweet."

"It smelled sweet?" Keller asked.

"Yeah, it smelled sweet, like candy."

"That's strange, did all of your team breath in the air?"

"Yes, they did."

"Oh no!" Keller exclaimed.

"What?" Rae asked.

"I couldn't reach Col. Shepard earlier in his comm, do you think he is having the same problems?"

"I don't know, see if Rodney has found him yet."

Keller tapped her comm, "Dr. McKay, this is Keller, have you found Col. Shepard?" Keller waited a few seconds then said, "He's not answering."

"He was on the planet too, maybe..."

"Marie! Get a team and find Col. Shepard and Dr. McKay right away." Marie nodded and motioned for a few nurses to follow her.

"Jen," Rae said, "What about Ronon and Teyla?"

Keller tapped her comm again and called their names. Nobody answered. "Marie! I'm coming with you, we need to locate everybody as quickly as possible, they may be having trouble breathing." Keller yelled to Marie as she and med team were getting ready to leave. "You going to be alright by yourself?" she asked Rae.

"I'll be fine, just find them."

"We will." Keller said confidently, "We will."

Rae stared at the door, willing Keller to come back and say everyone was fine and the comm system just wasn't working. But in her heart she knew better, John and the rest of his team was in trouble, and she was helpless to do anything about it. She hated it, she hated being so helpless. She wanted to be out there helping search for them. She had grow to care for the team in her one day here. Some people might think she is crazy, caring for people she barely knows but that's just the way she is. But John, her John, the boy she had grown up with and fell in love with was the main reason she was so stir crazy. She still loved him, even after all he had done to her, after all the hurt he put her through, she still loved him.

The sound of frantic voices pulled Rae from her thoughts. She watched as John, Rodney, Teyla, and Ronon were wheeled into the infirmary with people all around them. She watched as they tried to get them breathing again.

"Dr. Keller?" A nurse yelled. "I'm not getting any pulse!"

Rae's heart stopped as she watched Keller go to the nurse at John's side.

"Get him hooked up to a heart monitor fast!" Keller yelled. "And bring me a defibrillator quickly!"

A nurse rushed to do her bidding. Keller began to do CPR. As a nurse hooked up the heart monitor and another came with the defibrillator, a long beep could be heard from the monitor. Keller grabbed the paddles and set it for 200,

"Clear!" she yelled before placing the paddles on his now bare chest.

John's body arched as the charge ran through him. Still no pulse.

"Again!" Keller yelled as a nurse changed the charge to 300, "Clear!"

His body arched again, but still no pulse.

"Again!"

Rae closed her eyes as tears began coursing down her cheeks. All she could hear was that long steady beep.


	6. Chapter 6

**A/N: Revised chapter **

Chapter Six

As Rae woke up, she heard voices talking quietly.

"It was so close," Keller said, "I was so sure we had lost him but he's alive."

A nurse answered, but Rae didn't hear any of it, all she heard was "he's alive." He's alive...he's alive! He's really alive!

Rae forced her eyes open and saw him lying on the cot next to her. There were a lot of tubes attached to him but she could hear the heart monitor beeping.

"Oh Rae, you're awake." Rae turned her head and saw Keller smiling at her.

"He's alive?" Rae asked in a raspy voice.

"Yes, he's alive." Keller said.

Rae felt relieved. "Is he going to be okay?"

"Yes."

Rae smiled happily. "The others?"

"They're fine." Keller replied. "And so are you. You had a meltdown after Col. Shepard's heart stopped."

"What do you mean?" Rae asked.

"You freaked out." Keller replied. "You started screaming and thrashing. We had to sedate you."

"Oh," Rae said sheepishly. "uh who all heard that?"

"Most of the nursing staff, and I think Col. Shepard did too." Keller said, smiling.

"What do you mean?"

"I mean, when you starting screaming his name, his heart started beating again."

"What?!" Rae exclaimed.

"It's true. I think you two care a lot for each other, even if you don't want to admit it." Keller said, walking over to John's cot, checking his vitals. "He should wake up soon. Do you want to be alone?"

"Please." Rae said, looking over at John's sleeping form.

"Okay." Keller smiled, giving Rae's hand a squeeze. She walked out of the room.

Rae looked at John, memorizing every single detail. She couldn't believe how close she came to losing him. After all the searching she did to find him, after pulling a whole bunch of favors from the SGC and the Pentagon to have her transferred to Atlantis, she had to make peace with him soon. This job is dangerous and one never know whether a mission could be their last. Plus there was the fact-

"Rae?"

Rae was pulled from her thoughts by a hoarse voice. "John?" she asked, looking over at him.

"What happened?"

"The air on the planet we were on was poisonous, it stopped us from breathing and..." Rae stopped for a second, trying to keep the emotion out of her voice, "...you almost died." she finished with a whisper.

John looked at her for a moment, trying to read her face. "I almost died?" he asked.

"Yeah, you did."

They sat in silence for awhile until John asked, "The rest of my team?"

"Fine." Rae replied, then lapsed into silence again. The silence became more and more awkward until John spoke again,

"And you? Are you okay?"

Rae looked over at him with a half-smile on her face, "I'm okay."

"Just okay?" John asked, returning the smile.

"Yes, just okay."

Just then Dr. Keller walked into the room, "Oh Colonel, you're awake. Good. I have to run some tests on you, okay?"

"Okay." he answered.

A pair of nurses went and rolled John's cot out of the room. Keller waited until he was out of hearing range, then turned and asked Rae, "Have you told him?"

"Told him what?" Rae asked nonchalantly.

"I'm a doctor Rae, you can't hide it from me."

Rae sighed, "Eventually, we haven't spoken to each other in years, I don't think he even knew I was married."

"It must be tough" Keller sympathized.

"It is," Rae agreed. "I lose my husband and two days later I find out I'm pregnant."


	7. Chapter 7

**A/N: Revised chapter**

Chapter Seven

Rae sat in her room, looking over the latest Wraith schematics they had gotten from their last mission. She had been at Atlantis for two months now, settling in nicely. She has gotten to know almost every person on the base, especially Major Lorne. She had met him a week after she was let out of the infirmary, he ran into her, literally.

***Flashback***

_Rae was walking back from the mess hall reading a pad. She rounded a corner and felt herself hit what felt like a brick wall. She fell to the ground, pad falling from her hands._

_"Oh I'm sorry! Are you alright?"_

_Rae heard a male voice talking to her. "I think so." she said, shaking her head to clear her vision._

_"Here let me help you up." he said, extending his hand towards her._

_She took his hand and he pulled her up. Rae felt his arm slide around her waist to steady her as she fought to keep her balance. "Thank you." she said, pulling away as she got her balance._

_"No problem." he said. "I'm Major Lorne by the way." He stuck out his hand again._

_"Dr. Blake." Rae said, taking his hand and shaking it._

_"Hey you're the new doctor aren't you?"_

_"Yeah, that's me." Rae said, giving him a smile._

_"You kinda've had a rough time here so far huh?" he asked her, returning her smile._

_"Yeah, you could say that." Rae laughed._

_"How are you liking Atlantis so far then?" Lorne asked._

_"It's amazing, this city is so huge! It must be taking forever to explore it."_

_"Yeah we've been here almost five years and haven't seen it all." Lorne agreed._

_"I've only seen a part of it. I haven't had much time to explore. My first few weeks were spent in the infirmary and now Rodney has me looking over some schematics of the city so I can start helping him fix stuff." Rae said._

_"Well, maybe you should take some time off and explore." Lorne said._

_"I would, but I'm afraid I would get lost. The people I know are always so busy so I don't want to ask them to show me around." Rae said._

_"Well maybe I could." Lorne burst out._

_"What?" Rae asked, shocked._

_"If you would like, I could show you around."_

_"Aren't you busy too?"_

_"I can take some time off."_

_"Oh no, I couldn't ask you to do that."_

_"It would be my pleasure."_

_Rae looked at him then smiled and said, "Okay, but only because I really want to see the city."_

_"Of course." Lorne smiled._

***End Flashback***

Rae had gone and seen the city with Lorne. She learned that his first name was Evan and he liked to paint. They had seen each other several times after that, they enjoyed each other's company. Rumors that they were dating were spreading throughout the city. Rae didn't know what to think. On one hand Evan was a very attractive man and she enjoyed talking to him. On the other hand, she still had hidden feelings for John. She hadn't told either that she had been married or that she was with child. She knew that she was going to start showing soon. She had to find a way to tell them.

Oh how she missed her husband. Alex had been a kind man, her best friend, she loved him so much. She had met him when she had starting working at the SGC six years ago, they had married three years later. They hadn't wanted kids right away, their jobs being too dangerous to consider having kids. They were about to retire from the SGC so they could have kids. Alex had to go on one last mission before he was done, so he did and came back as a medical emergency. He had been rushed to the infirmary and died an hour later. Rae had been by his side when he died, his last words being,

_"I love you, don't forget to be happy."_

She hadn't cried, instead she asked the SGC for her position back, and they had given it to her, against their better judgment. A few months later she had starting looking for John, looking for the comfort he was once able to give her. The fact that she was pregnant only deepened her grief, her child was all that she had left of her husband.

Rae heard her door beep, indicating that someone was at the door. She sighed and got up, tossing her pad on the bed as she did so. She opened the door to see Lorne standing outside.

"Hey Evan." she greeted him.

"Hey Rae," he said back. "hey I was, uh, wondering if you were interested in getting a late supper, I know you haven't eaten."

Rae smiled, "Yeah, I've been so busy looking over the data we got from our last mission that I forgot to eat I guess."

"So dinner?" Lorne asked, holding out his arm for her to take.

Rae thought for a moment then took his arm. "Sure why not?" she said.

They walked off towards the mess hall, not knowing that John was watching from a distance.


	8. Chapter 8

**A/N: Revised chapter.**

Chapter Eight

"So Rae, how are you settling in?" John asked Rae as they were getting ready for another mission.

"Great, everyone here is really nice." she said, smiling.

"Especially Major Lorne?" he asked.

"What?" Rae asked, confused.

"I said, isn't Major Lorne being extremely nice to you? I mean, I've heard you two have been spending a lot of time with each other." John looked at Rae, trying to gauge her reaction.

"Major Lorne has been nice to me yes...is that a problem?" Rae asked, looking even more confused.

"No, no problem at all, I just need to know if there is more than a friendship between my second in command and one of the scientists." John explained.

"John, have you been listening to rumors?" Rae chided him

"It's my business to know."

Rae smiled, "There is nothing going on between me and Major Lorne, we're just friends."

John nodded, "That's all I needed to know."

"Okay" Rae said.

Rae groaned as they walked back through the gate, "Honestly! Is it really do hard for you not to go all Captain Kirk on every pretty girl in TWO galaxies?"

"Hey! I did not go all "Captain Kirk" on Leia, I was just being nice." John argued back.

"Uh huh."

Rae sighed as she started to take her equipment off. "Hey Teyla, are we still on for dinner later?" Rae asked.

"I'm sorry but I had forgotten that Kannan is gone tonight and therefore I have to watch Torren." Teyla said apologetically.

"Hey bring him along, I haven't seen him in a while." Rae said.

"Alright." Teyla smiled. "I will see you later then?"

"Later." Rae said waving as she walked out of the room.

"Dr. Blake, will you please report to the infirmary?" Dr. Keller's voice came over Rae's comm.

She tapped it, "On my way Jen, what's up?"

"I have some news." Keller said.

"Oh really, what kind of news?" Rae asked.

"You'll see when you get here."

Rae shook her head and sighed. She began walking walked to the infirmary. As she rounded a corner she ran into Major Lorne, again.

"Ow!" Rae yelped. "Seriously! What do you eat? Bricks?"

"Sorry!" Lorne said, looking amused. "You know," he said. "we really have got to stop running into each other."

"Oh ha ha!" Rae laughed mockingly. "Such a joker."

"So where are you headed?" Lorne asked Rae.

"To the infirmary."

"What? I didn't hurt you that bad, did I?"

"No, I was heading there before you ran into me."

"Oh good. Why are you going then?"

"Not quite sure, Dr. Keller said she had some news for me."

"Do you want me to come with you?"

"That's sweet Evan, but no thanks, I'm good."

"Alright, see ya later?"

"Later." Rae shook her head as Lorne walked away, "You have got to stop that." she scolded herself as she starting walking to the infirmary again.

"Hey Jen what's up?" Rae asked as she walked into the infirmary.

"Come in my office." Keller said.

"Is something wrong?" Rae asked as she took a seat in Keller's office.

"No nothing's wrong, I just thought you wouldn't want this news to be overheard." Keller said.

"What news?" Rae asked.

"Rae, I was given the pictures from your last ultrasound a few hours ago, and.." Keller paused as she got ready to drop a bombshell. "Rae, you're going to have twins."


	9. Chapter 9

**A/N: Hey guys here's chapter nine! hope you like it. I changed the way I wrote it because I was told this would be easier to understand. I'm going back and changing all the other chapters like this. Enjoy!**

Chapter Nine

Rae stared at Keller in shock. "Twins?!" she yelled.

"Yes, twins. It's too early to tell whether they're boys or girls or one of each." Keller said.

Rae couldn't believe it, twins? This was more than she could handle. "Thank you for telling me." she said stiffly to Keller. "Now if you don't mind I'm going to go be alone for awhile."

"Of course." Keller said, "I'm here of you need someone to talk to."

"Thanks Jen." Rae said with a bit more warmth in her voice.

Rae turned and walked out of the room. On the outside she looked very calm, but on the inside she was freaking out. She was going to have twins. Oh boy. She leaned against a wall. Twins. This was not what she expected. She needed to talk to someone, but she didn't know who. She wanted so badly to tell John, but she was scared, what would he think of her?

"Twins." she whispered. She looked both ways down the hallway, it was empty. She slid down the wall to the floor. She pulled her knees close to her chest and buried her face into them. She stayed like that until she heard a voice call her name,

"Rae?" She looked up to see John staring at her. "Hey, what's up?" he asked her. "Keller called me on my radio and said that she couldn't contact you and that I would be the best person to find you. What's going on?"

Rae wiped the tears from her face, "Nothing, everything's fine." she said.

"Everything's fine? Don't give me that bull Rae. I may not have spoken to you in a long time but I've still known you your whole life, don't tell me nothing's wrong." John said, kneeling down next to her.

Rae stared at him for awhile the fell into him and started crying.

John didn't know what to do, here was Rae, who he was still only on speaking terms with, crying into his chest. He wrapped his arms around her and pulled her closer. "What's wrong?" he whispered into her hair.

"Oh John, I've missed you." she sobbed into his shirt.

What?! She missed him?! "I've missed you too Rae." he said.

"I have so much to tell you." she said, pulling herself away she so she could look at him.

"Okay, do you want to go to your quarters?" he asked her, unsure of what to do. It had been a long time since she told him anything.

"Sure." John helped her to her feet then began walking towards her room. When they got there, they sat on her bed and John waited for her to say something.

"John," Rae began, then stopped, then started again. "I don't know if you've ever met Alex Sanders?"

"No, name doesn't ring a bell."

"Well he worked for the SGC, he was the leader of SG-6. I met him when I was assigned to go with his team on a mission. We got along really well and I ended up marrying him." She paused to take a breath.

John looked at her in shock, she was MARRIED?! Wait, then why wasn't she wearing a wedding ring...

"He was killed in action on his last mission." Rae continued, "Both he and I were going to leave the SGC so we could have kids. He only had one more mission and-" Rae broke down and started crying again.

John didn't know what to do, he was still in shock that she had been married. That she had loved someone enough to be willing to spend the rest of her life with him. He reached over and pulled Rae into his arms. "Hey, I understand what it's like to loose a loved one."

"Thanks, but that's not all of it." Rae said, pulling away so she could look at him.

"What is it?" "John, I'm going to have his kids."

"What?" Now he was even more shocked.

"John, I'm pregnant, with twins."

"What?" John asked again in now utter shock. "You're pregnant?!"

"Yes." Rae said quietly.

John stood up. "I can't believe this!" he shouted, pacing around the room. "You know, I had the same problem with Teyla? She decided it would be okay to go on missions even though she was pregnant!"

"I was going to stop going on missions at the end of the week."

"Well don't bother," John said in a deadly quiet voice. "you are no longer going on any missions."

"Okay." Rae said, looking down at her folded hands.

John stared at her for a while, mentally kicking himself. Rae trusted him enough, after all he'd done to her, to tell him this and what does he do? He yells at her. John groaned then sat down next to her.

"Hey Rae? I'm sorry, I overreacted, forgive me?"

Rae looked up, smiling. "Of course."

John breathed a sigh of relief. "And Rae?"

"Yes John?"

"Can you forgive me for hurting you in high school?"

Rae's smile became even bigger. "Oh John, I forgave you for that a long time ago."

They both smiled at each other and Rae said, "Oh come here ya big lug."

John laughed then put his arms around her again, a huge smile on his face.

**A/N: Awwww now their friends again :) Now Rae will have the hard decision of choosing between John or Lorne...or will she? And she still has to tell Lorne she is going to have kids...**


End file.
